[gmx-users] Urey Bradley Parameters in GROMACS

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 26 18:18:50 CET 2010

> Hello everyone,
> I have a pdb file of a solvent molecule for which I need to generate a 
> .itp file. 
> The solute is modeled using AMBER and I have topology file generated 
> using amb2gmx.sh.
> However, the solvent molecule has Urey Bradley parameters specified. 

Then, wouldn't the CHARMM force field be more appropriate?  Angles in AMBER do 
not usually include these terms.

> Since, I am new to GROMACS I wish to learn as to how an .itp could be 
> created from scratch to incorporate the aforesaid parameters.

Please see the manual, specifically Chapter 5 and Table 5.4; as long as you have 
sound justification for using those parameters within the chosen force field, 
you can easily add them to the [angles] directive of the topology.


> Thanks,
> Pradeep 


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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